Man pages for ORFik
Open Reading Frames in Genomics

addCdsOnLeaderEndsExtends leaders downstream
addNewTSSOnLeadersAdd cage max peaks as new transcript start sites for each 5'...
allFeaturesHelperCalculate the features in computeFeatures function
artificial.orfsCreate small artificial orfs from cds
assignAnnotationsOverlaps GRanges object with provided annotations.
assignFirstExonsStartSiteReassign the start positions of the first exons per group in...
assignLastExonsStopSiteReassign the stop positions of the last exons per group
assignTSSByCageInput a txdb and add a 5' leader for each transcript, that...
asTXMap genomic to transcript coordinates by reference
bamVarNameGet library variable names from ORFik 'experiment'
bamVarNamePickerGet variable name per filepath in experiment
bedToGRConverts bed style data.frame to Granges
cellLineNamesGet cell-line name variants
changePointAnalysisGet the offset for specific RiboSeq read width
checkRFPHelper Function to check valid RFP input
checkRNAHelper Function to check valid RNA input
codonSumsPerGroupGet read hits per codon reads by sum of existing scores
collapseDuplicatedReadsCollapse duplicated reads
collapseDuplicatedReads-GAlignmentPairs-methodCollapse duplicated reads
collapseDuplicatedReads-GAlignments-methodCollapse duplicated reads
collapseDuplicatedReads-GRanges-methodCollapse duplicated reads
collapse.fastqVery fast fastq/fasta collapser
combn.pairsCreate all unique combinations pairs possible
computeFeaturesGet all possible features in ORFik
computeFeaturesCageGet all possible features in ORFik
conditionNamesGet condition name variants
configRead directory config for ORFik experiments
config.experSet directories for experiment
config.saveSave/update directory config for ORFik experiments
convertLibsConverted format of NGS libraries
convertToOneBasedRangesConvert a GRanges Object to 1 width reads
correlation.plotsCorrelation plots between all samples
countOverlapsWCountOverlaps with weights
countTableExtract count table directly from experiment
countTable_regionsMake a list of count matrices from experiment
coverageByTranscriptWcoverageByTranscript with weights
coverageGroupingsGet grouping for a coverage table in ORFik
coverageHeatMapCreate a heatmap of coverage
coveragePerTilingGet coverage per group
coverageScoringsAdd a coverage scoring scheme
create.experimentCreate a ORFik 'experiment'
defineIsoformOverlaps GRanges object with provided annotations.
defineTrailerDefines trailers for ORF.
detectRibosomeShiftsDetect ribosome shifts
disengagementScoreDisengagement score (DS)
distToCdsGet distances between ORF ends and starts of their...
distToTSSGet distances between ORF Start and TSS of its transcript
download.ebiFaster download of fastq files
download.SRADownload read libraries from SRA
download.SRA.metadataDownloads metadata from SRA
downstreamFromPerGroupGet rest of objects downstream (inclusive)
downstreamNRestrict GRangesList
downstreamOfPerGroupGet rest of objects downstream (exclusive)
DTEG.analysisRun differential TE analysis
DTEG.plotPlot DTEG result
entropyPercentage of maximum entropy
exists.ftp.file.fastA copy of biomartr ftp check
experiment-classexperiment class definition
experiment.colorsDecide color for libraries by grouping
export.bed12Export as bed12 format
export.bedoStore GRanges object as .bedo
export.bedocStore GAlignments object as .bedoc
export.ofstStore GRanges / GAlignments object as .ofst
export.ofst-GAlignmentPairs-methodStore GRanges / GAlignments object as .ofst
export.ofst-GAlignments-methodStore GRanges / GAlignments object as .ofst
export.ofst-GRanges-methodStore GRanges / GAlignments object as .ofst
export.wiggleExport as wiggle format
extendLeadersExtend the leaders transcription start sites.
extendsTSSexonsExtend first exon of each transcript with length specified
extendTrailersExtend the Trailers transcription stop sites
filepathGet filepaths to ORFik experiment
filterCageFilter peak of cage-data by value
filterExtremePeakGenesFilter out transcript by a median filter
filterTranscriptsFilter transcripts by lengths
filterUORFsRemove uORFs that are false CDS hits
fimportLoad any type of sequencing reads
findFaConvenience wrapper for Rsamtools FaFile
findFromPathFind all candidate library types filenames
findLibrariesInFolderGet all library files in folder/folders of given types
findMapORFsFind ORFs and immediately map them to their genomic...
findMaxPeaksFind max peak for each transcript, returns as data.table,...
findNewTSSFinds max peaks per trancsript from reads in the cagefile
findNGSPairsFind pair of forward and reverse strand wig / bed files and...
findORFsFind Open Reading Frames.
findORFsFastaFinds Open Reading Frames in fasta files.
findPeaksPerGeneFind peaks per gene
findUORFsFind upstream ORFs from transcript annotation
find_url_ebiLocates and check if fastq files exists in ebi
firstEndPerGroupGet first end per granges group
firstExonPerGroupGet first exon per GRangesList group
firstStartPerGroupGet first start per granges group
flossFragment Length Organization Similarity Score
footprints.analysisPre shifting plot analysis
fpkmCreate normalizations of overlapping read counts.
fpkm_calcCreate normalizations of read counts
fractionLengthFraction Length
fread.bedLoad bed file as GRanges
gcContentGet GC content
getGAlignmentsInternal GAlignments loader from fst data.frame
getGAlignmentsPairsInternal GAlignmentPairs loader from fst data.frame
getGenomeAndAnnotationDownload genome (fasta), annotation (GTF) and contaminants
get_genome_fastaDownload genome (fasta), annotation (GTF) and contaminants
get_genome_gtfDownload genome (fasta), annotation (GTF) and contaminants
getGRangesInternal GRanges loader from fst data.frame
getNGenesCoverageGet number of genes per coverage table
get_noncoding_rnaDownload genome (fasta), annotation (GTF) and contaminants
get_phix_genomeDownload genome (fasta), annotation (GTF) and contaminants
get_silva_rRNADownload Silva SSU & LSU sequences
getWeightsGet weights from a subject GenomicRanges object
groupGRangesByGroup GRanges
groupingsGet number of ranges per group as an iteration
gSortSort a GRangesList, helper.
hasHitsHits from reads
heatMapLCoverage heatmap of multiple libraries
heatMapRegionCreate coverage heatmaps of specified region
heatMap_singleCoverage heatmap of single libraries
import.bedoLoad GRanges object from .bedo
import.bedocLoad GAlignments object from .bedoc
importGtfFromTxdbImport the GTF / GFF that made the txdb
import.ofstLoad GRanges / GAlignments object from .ofst
initiationScoreGet initiation score for a GRangesList of ORFs
insideOutsideORFInside/Outside score (IO)
install.fastpDownload and prepare fastp trimmer
install.sratoolkitDownload sra toolkit
is.grlHelper function to check for GRangesList
is.gr_or_grlHelper function to check for GRangesList or GRanges class
isInFrameFind frame for each orf relative to cds
is.ORFCheck if all requirements for an ORFik ORF is accepted.
isOverlappingFind frame for each orf relative to cds
isPeriodicFind if there is a periodicity of 3 in the vector
is.rangeHelper function to check for ranged object
kozakHeatmapMake sequence region heatmap relative to scoring
kozak_IR_rankingRank kozak initiation sequences
kozakSequenceScoreMake a score for each ORFs start region by proximity to Kozak
lastExonEndPerGroupGet last end per granges group
lastExonPerGroupGet last exon per GRangesList group
lastExonStartPerGroupGet last start per granges group
libNamesGet library name variants
libraryTypesWhich type of library type in 'experiment'?
list.experimentsList current experiment available
loadRegionLoad transcript region
loadRegionsGet all regions of transcripts specified to environment
loadTranscriptTypeLoad transcripts of given biotype
loadTxdbGeneral loader for txdb
longestORFsGet longest ORF per stop site
mainNamesGet main name from variant name
makeExonRanksMake grouping by exons ranks
makeORFNamesMake ORF names per orf
makeSummarizedExperimentFromBamMake a count matrix from a library or experiment
mapToGRangesMap orfs to genomic coordinates
matchColorsMatch coloring of coverage plot
matchNamingMatch naming of GRangesList
matchSeqStyleA wrapper for seqlevelsStyle
mergeFastqMerge groups of Fastq /Fasta files
metaWindowCalculate meta-coverage of reads around input GRanges/List...
nrow-experiment-methodInternal nrow function for ORFik experiment Number of runs in...
numCodonsGet number of codons
numExonsPerGroupGet list of the number of exons per group
optimizeReadsFind optimized subset of valid reads
orfIDGet id's for each orf
ORFik-packageORFik for analysis of open reading frames.
ORFikQCA post Alignment quality control of reads
ORFik.template.experimentAn ORFik experiment to see how it looks
orfScoreGet ORFscore for a GRangesList of ORFs
organism.dfGet organism of the ORFik experiment
outputLibsOutput bam/bed/bedo/bedoc/ofst/wig files to R as variables
pasteDirA paste function for directories Makes sure slashes are...
percentage_to_ratioConvert percentage to ratio of 1
plotHelperHelper function for coverage plots
pmapFromTranscriptFFaster pmapFromTranscript
pmapToTranscriptFFaster pmapToTranscript
prettyScoringPrettify scoring name
pseudo.transformTransform object
pSitePlotPlot area around TIS as histogram
QC_count_tablesCreate count table info for QC report
QCplotsCorrelation and coverage plots for ORFikQC
QCreportA post Alignment quality control of reads
QCstatsLoad ORFik QC Statistics report
QCstats.plotMake plot of ORFik QCreport
rankOrderORF rank in transcripts
readBamCustom bam reader
read.experimentRead ORFik 'experiment'
readLengthTableMake table of readlengths
readWidthsGet read widths
readWigCustom wig reader
reassignTSSbyCageReassign all Transcript Start Sites (TSS)
reassignTxDbByCageInput a txdb and reassign the TSS for each transcript by CAGE
reduceKeepAttrReduce GRanges / GRangesList
regionPerReadLengthFind proportion of reads per position per read length in...
remakeTxdbExonIdsGet new exon ids after update of txdb
remove.experimentsRemove bam/bed/wig files load in R as variables
remove.file_extRemove file extension of path
removeMetaColsRemoves meta columns
removeORFsWithinCDSRemove ORFs that are within cds
removeORFsWithSameStartAsCDSRemove ORFs that have same start site as the CDS
removeORFsWithSameStopAsCDSRemove ORFs that have same stop site as the CDS
removeORFsWithStartInsideCDSRemove ORFs that have start site within the CDS
removeTxdbExonsRemove exons in txList that are not in fiveUTRs
removeTxdbTranscriptsRemove specific transcripts in txdb List
rename.SRA.filesRename SRA files from metadata
repNamesGet replicate name variants
restrictTSSByUpstreamLeaderRestrict extension of 5' UTRs to closest upstream leader end
reverseMinusStrandPerGroupReverse minus strand
RiboQC.plotQuality control for pshifted Ribo-seq data
ribosomeReleaseScoreRibosome Release Score (RRS)
ribosomeStallingScoreRibosome Stalling Score (RSS)
rnaNormalizeNormalize a data.table of coverage by RNA seq per position
save.experimentSave 'experiment' to disc
savePlotHelper function for writing plots to disc
scaledWindowPositionsScale (bin) windows to a meta window of given size
scoreSummarizedExperimentHelper function for makeSummarizedExperimentFromBam
seqnamesPerGroupGet list of seqnames per granges group
shiftFootprintsShift footprints by selected offsets
shiftFootprintsByExperimentShift footprints of each file in experiment
shiftPlotsPlot shifted heatmaps per library
shifts.loadLoad the shifts from experiment
show-experiment-methodexperiment show definition
simpleLibsConverted format of NGS libraries
sortPerGroupSort a GRangesList
splitIn3TxCreate binned coverage of transcripts, split into the 3...
stageNamesGet stage name variants
STAR.align.folderAlign all libraries in folder with STAR
STAR.align.singleAlign single or paired end pair with STAR
STAR.allsteps.multiQCCreate STAR multiQC plot and table
STAR.indexCreate STAR genome index
STAR.installDownload and prepare STAR
STAR.multiQCCreate STAR multiQC plot and table
STAR.remove.crashed.genomeRemove crashed STAR genome
startCodonsGet the Start codons(3 bases) from a GRangesList of orfs...
startDefinitionReturns start codon definitions
startRegionStart region as GRangesList
startRegionCoverageStart region coverage
startRegionStringGet start region as DNA-strings per GRanges group
startSitesGet the start sites from a GRangesList of orfs grouped by...
stopCodonsGet the Stop codons (3 bases) from a GRangesList of orfs...
stopDefinitionReturns stop codon definitions
stopRegionStop region as GRangesList
stopSitesGet the stop sites from a GRangesList of orfs grouped by orfs
strandBoolGet logical list of strands
strandPerGroupGet list of strands per granges group
subsetCoverageSubset GRanges to get coverage.
subsetToFrameSubset GRanges to get desired frame.
te.plotTranslational efficiency plots
te_rna.plotTranslational efficiency plots
te.tableCreate a TE table
tile1Tile each GRangesList group to 1-base resolution.
tissueNamesGet tissue name variants
topMotifTOP Motif detection
TOP.Motif.ecdfTOP Motif ecdf plot
transcriptWindowMake 100 bases size meta window for all libraries in...
transcriptWindow1Meta coverage over all transcripts
transcriptWindowPerHelper function for transcriptWindow
translationalEffTranslational efficiency
trim_detectionAdd trimming info to QC report
trimming.tableCreate trimming table
txNamesGet transcript names from orf names
txNamesToGeneNamesConvert transcript names to gene names
txSeqsFromFaGet transcript sequence from a GrangesList and a faFile or...
uniqueGroupsGet the unique set of groups in a GRangesList
uniqueOrderGet unique ordering for GRangesList groups
unlistGrlSafe unlist
uORFSearchSpaceCreate search space to look for uORFs
updateTxdbRanksUpdate exon ranks of exon data.frame inside txdb object
updateTxdbStartSitesUpdate start sites of leaders
upstreamFromPerGroupGet rest of objects upstream (inclusive)
upstreamOfPerGroupGet rest of objects upstream (exclusive)
validateExperimentsValidate ORFik 'experiment'
validGRLHelper Function to check valid GRangesList input
validSeqlevelsHelper function to find overlaping seqlevels
widthPerGroupGet list of widths per granges group
windowCoveragePlotGet meta coverage plot of reads
windowPerGroupGet window region of GRanges object
windowPerReadLengthFind proportion of reads per position per read length in...
windowPerTranscriptGet a binned coverage window per transcript
xAxisScalerScale x axis correctly
yAxisScalerScale y axis correctly
ORFik documentation built on March 27, 2021, 6 p.m.